tag:blogger.com,1999:blog-3599722177679860131.post7352341410409363468..comments2024-01-03T10:01:29.738+01:00Comments on Chemical Quantum Images: Simplified molecular input line entry specificationFelixhttp://www.blogger.com/profile/05138335803929997277noreply@blogger.comBlogger9125tag:blogger.com,1999:blog-3599722177679860131.post-68097048912551026322008-04-09T02:18:00.000+01:002008-04-09T02:18:00.000+01:00Emacs isn't obscure. It's the best thing ever. E...Emacs isn't obscure. It's <I>the best</I> thing ever. Ever.<BR/><BR/>/soapboxShawn Wilkinsonhttps://www.blogger.com/profile/18308205724057373941noreply@blogger.comtag:blogger.com,1999:blog-3599722177679860131.post-39450073425643792392008-03-22T19:11:00.000+01:002008-03-22T19:11:00.000+01:00A couple of responses to lightnir's comment. Alth...A couple of responses to lightnir's comment. <BR/><BR/>Although SMARTS notation can be used to specify how molecules should be overlaid, it goes well beyond that. The SMARTS language enables powerful and general definition of substructures. And that is the basis of chemistry. BTW good to see the use of recursive SMARTS in your example. <BR/><BR/>Although canonicalisation of SMILES is very useful, you are not obliged to write SMILES in their canonical form. If you need to build structures from scratch, it's usually quicker to type them in as SMILES (hence my reference to emacs). This makes it easy to force a particular ordering of atoms since many 3D structure generators will maintain SMILES order. If you're doing covalent docking with something like GOLD, you will typically need to have ordered the molecules so that the covalent link atom always occurs at a fixed point (e.g. first atom) in the molecule.Georg-Martin Krapperhttps://www.blogger.com/profile/15416686863175197568noreply@blogger.comtag:blogger.com,1999:blog-3599722177679860131.post-66750420246216472792008-03-21T18:04:00.000+01:002008-03-21T18:04:00.000+01:00Felix: Why wait if you can learn it faster by your...Felix: Why wait if you can learn it faster by yourself. You may be interested in <A HREF="http://lightnir.blogspot.com/2008/03/testcode.html" REL="nofollow">this </A> short article.<BR/>GMC2007: The emacs part sounds like fun to me ]:)Lightnirhttps://www.blogger.com/profile/16789348893952913132noreply@blogger.comtag:blogger.com,1999:blog-3599722177679860131.post-47338171336455462042008-03-20T23:35:00.000+01:002008-03-20T23:35:00.000+01:00One of the coolest things about SMILES is that the...One of the coolest things about SMILES is that there are algorithms for generating the canonical SMILES for a molecule. In general you can write a number of equally valid SMILES for a molecule. The canonicalisation algorithms identify one of these SMILES as the canonical SMILES. You can identify duplicate molecules in databases by simple string matching. SMILES notation also makes it very easy to build molecular models using obscure modelling tools such as the emacs editor.Georg-Martin Krapperhttps://www.blogger.com/profile/15416686863175197568noreply@blogger.comtag:blogger.com,1999:blog-3599722177679860131.post-65221090551580672092008-03-19T10:27:00.000+01:002008-03-19T10:27:00.000+01:00I am waiting until they teach me that in class ......I am waiting until they teach me that in class ...Felixhttps://www.blogger.com/profile/05138335803929997277noreply@blogger.comtag:blogger.com,1999:blog-3599722177679860131.post-60557011627483738982008-03-19T08:09:00.000+01:002008-03-19T08:09:00.000+01:00You find drawing structures by using SMILES cool? ...You find drawing structures by using SMILES cool? Yeah, right... When you want to do something really cool try superimposing molecules by using Smiles Arbitrary Target Specification (SMARTS). It's a kind of query language based on SMILES that allows you to search molecule fragments within SMILES strings. Check <A HREF="http://openbabel.org/wiki/Obfit" REL="nofollow">obfit</A> from the Open Babel package for more info.Lightnirhttps://www.blogger.com/profile/16789348893952913132noreply@blogger.comtag:blogger.com,1999:blog-3599722177679860131.post-35547849216031856332008-03-18T12:28:00.000+01:002008-03-18T12:28:00.000+01:00Ψ*Ψ: I am glad they forced me into that ch...Ψ*Ψ: I am glad they forced me into that cheminformatics class, and told me what it's about<BR/><BR/>egon: it seems cool that so much is open source these days. maybe eventually I will use SMILES, this was just for curiosityFelixhttps://www.blogger.com/profile/05138335803929997277noreply@blogger.comtag:blogger.com,1999:blog-3599722177679860131.post-85408299164402137432008-03-18T08:15:00.000+01:002008-03-18T08:15:00.000+01:00It might interest you that OpenSMILES.org is worki...It might interest you that <A HREF="http://OpenSMILES.org" REL="nofollow">OpenSMILES.org</A> is working on a open standard for SMILES.Egon Willighagenhttps://www.blogger.com/profile/07470952136305035540noreply@blogger.comtag:blogger.com,1999:blog-3599722177679860131.post-68234570262615048972008-03-18T01:16:00.000+01:002008-03-18T01:16:00.000+01:00Cool! I always kinda wondered how that worked.Cool! I always kinda wondered how that worked.Ψ*Ψhttps://www.blogger.com/profile/15089754859676425655noreply@blogger.com